Job ID = 2001687 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,411,870 reads read : 26,411,870 reads written : 26,411,870 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:34 26411870 reads; of these: 26411870 (100.00%) were unpaired; of these: 569522 (2.16%) aligned 0 times 19772393 (74.86%) aligned exactly 1 time 6069955 (22.98%) aligned >1 times 97.84% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1739892 / 25842348 = 0.0673 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 08:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 08:56:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:56:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 08:56:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:56:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 08:57:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:57:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:57:08: 1000000 INFO @ Fri, 05 Jul 2019 08:57:09: 1000000 INFO @ Fri, 05 Jul 2019 08:57:11: 1000000 INFO @ Fri, 05 Jul 2019 08:57:17: 2000000 INFO @ Fri, 05 Jul 2019 08:57:17: 2000000 INFO @ Fri, 05 Jul 2019 08:57:20: 2000000 INFO @ Fri, 05 Jul 2019 08:57:25: 3000000 INFO @ Fri, 05 Jul 2019 08:57:26: 3000000 INFO @ Fri, 05 Jul 2019 08:57:30: 3000000 INFO @ Fri, 05 Jul 2019 08:57:35: 4000000 INFO @ Fri, 05 Jul 2019 08:57:36: 4000000 INFO @ Fri, 05 Jul 2019 08:57:40: 4000000 INFO @ Fri, 05 Jul 2019 08:57:43: 5000000 INFO @ Fri, 05 Jul 2019 08:57:44: 5000000 INFO @ Fri, 05 Jul 2019 08:57:49: 5000000 INFO @ Fri, 05 Jul 2019 08:57:52: 6000000 INFO @ Fri, 05 Jul 2019 08:57:53: 6000000 INFO @ Fri, 05 Jul 2019 08:57:59: 6000000 INFO @ Fri, 05 Jul 2019 08:58:01: 7000000 INFO @ Fri, 05 Jul 2019 08:58:01: 7000000 INFO @ Fri, 05 Jul 2019 08:58:09: 7000000 INFO @ Fri, 05 Jul 2019 08:58:09: 8000000 INFO @ Fri, 05 Jul 2019 08:58:10: 8000000 INFO @ Fri, 05 Jul 2019 08:58:17: 9000000 INFO @ Fri, 05 Jul 2019 08:58:19: 8000000 INFO @ Fri, 05 Jul 2019 08:58:19: 9000000 INFO @ Fri, 05 Jul 2019 08:58:24: 10000000 INFO @ Fri, 05 Jul 2019 08:58:28: 9000000 INFO @ Fri, 05 Jul 2019 08:58:28: 10000000 INFO @ Fri, 05 Jul 2019 08:58:32: 11000000 INFO @ Fri, 05 Jul 2019 08:58:38: 10000000 INFO @ Fri, 05 Jul 2019 08:58:38: 11000000 INFO @ Fri, 05 Jul 2019 08:58:40: 12000000 INFO @ Fri, 05 Jul 2019 08:58:48: 13000000 INFO @ Fri, 05 Jul 2019 08:58:48: 12000000 INFO @ Fri, 05 Jul 2019 08:58:48: 11000000 INFO @ Fri, 05 Jul 2019 08:58:55: 14000000 INFO @ Fri, 05 Jul 2019 08:58:58: 13000000 INFO @ Fri, 05 Jul 2019 08:58:58: 12000000 INFO @ Fri, 05 Jul 2019 08:59:03: 15000000 INFO @ Fri, 05 Jul 2019 08:59:07: 14000000 INFO @ Fri, 05 Jul 2019 08:59:08: 13000000 INFO @ Fri, 05 Jul 2019 08:59:11: 16000000 INFO @ Fri, 05 Jul 2019 08:59:17: 15000000 INFO @ Fri, 05 Jul 2019 08:59:18: 14000000 INFO @ Fri, 05 Jul 2019 08:59:19: 17000000 INFO @ Fri, 05 Jul 2019 08:59:26: 16000000 INFO @ Fri, 05 Jul 2019 08:59:27: 18000000 INFO @ Fri, 05 Jul 2019 08:59:28: 15000000 INFO @ Fri, 05 Jul 2019 08:59:35: 19000000 INFO @ Fri, 05 Jul 2019 08:59:36: 17000000 INFO @ Fri, 05 Jul 2019 08:59:37: 16000000 INFO @ Fri, 05 Jul 2019 08:59:43: 20000000 INFO @ Fri, 05 Jul 2019 08:59:46: 18000000 INFO @ Fri, 05 Jul 2019 08:59:47: 17000000 INFO @ Fri, 05 Jul 2019 08:59:51: 21000000 INFO @ Fri, 05 Jul 2019 08:59:55: 19000000 INFO @ Fri, 05 Jul 2019 08:59:56: 18000000 INFO @ Fri, 05 Jul 2019 09:00:01: 22000000 INFO @ Fri, 05 Jul 2019 09:00:05: 20000000 INFO @ Fri, 05 Jul 2019 09:00:06: 19000000 INFO @ Fri, 05 Jul 2019 09:00:09: 23000000 INFO @ Fri, 05 Jul 2019 09:00:14: 21000000 INFO @ Fri, 05 Jul 2019 09:00:16: 20000000 INFO @ Fri, 05 Jul 2019 09:00:17: 24000000 INFO @ Fri, 05 Jul 2019 09:00:18: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:00:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:00:18: #1 total tags in treatment: 24102456 INFO @ Fri, 05 Jul 2019 09:00:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:00:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 09:00:19: #1 tags after filtering in treatment: 24102283 INFO @ Fri, 05 Jul 2019 09:00:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:00:19: #1 finished! INFO @ Fri, 05 Jul 2019 09:00:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:00:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:00:24: #2 number of paired peaks: 58330 INFO @ Fri, 05 Jul 2019 09:00:24: start model_add_line... INFO @ Fri, 05 Jul 2019 09:00:24: 22000000 INFO @ Fri, 05 Jul 2019 09:00:24: start X-correlation... INFO @ Fri, 05 Jul 2019 09:00:24: end of X-cor INFO @ Fri, 05 Jul 2019 09:00:24: #2 finished! INFO @ Fri, 05 Jul 2019 09:00:24: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 09:00:24: #2 alternative fragment length(s) may be 1,133,295,501 bps INFO @ Fri, 05 Jul 2019 09:00:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.05_model.r INFO @ Fri, 05 Jul 2019 09:00:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:00:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:00:25: 21000000 INFO @ Fri, 05 Jul 2019 09:00:34: 23000000 INFO @ Fri, 05 Jul 2019 09:00:35: 22000000 INFO @ Fri, 05 Jul 2019 09:00:44: 24000000 INFO @ Fri, 05 Jul 2019 09:00:45: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:00:45: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:00:45: #1 total tags in treatment: 24102456 INFO @ Fri, 05 Jul 2019 09:00:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:00:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 09:00:45: 23000000 INFO @ Fri, 05 Jul 2019 09:00:45: #1 tags after filtering in treatment: 24102283 INFO @ Fri, 05 Jul 2019 09:00:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:00:45: #1 finished! INFO @ Fri, 05 Jul 2019 09:00:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:00:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:00:50: #2 number of paired peaks: 58330 INFO @ Fri, 05 Jul 2019 09:00:50: start model_add_line... INFO @ Fri, 05 Jul 2019 09:00:51: start X-correlation... INFO @ Fri, 05 Jul 2019 09:00:51: end of X-cor INFO @ Fri, 05 Jul 2019 09:00:51: #2 finished! INFO @ Fri, 05 Jul 2019 09:00:51: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 09:00:51: #2 alternative fragment length(s) may be 1,133,295,501 bps INFO @ Fri, 05 Jul 2019 09:00:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.10_model.r INFO @ Fri, 05 Jul 2019 09:00:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:00:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:00:55: 24000000 INFO @ Fri, 05 Jul 2019 09:00:56: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:00:56: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:00:56: #1 total tags in treatment: 24102456 INFO @ Fri, 05 Jul 2019 09:00:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:00:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 09:00:57: #1 tags after filtering in treatment: 24102283 INFO @ Fri, 05 Jul 2019 09:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:00:57: #1 finished! INFO @ Fri, 05 Jul 2019 09:00:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:01:02: #2 number of paired peaks: 58330 INFO @ Fri, 05 Jul 2019 09:01:02: start model_add_line... INFO @ Fri, 05 Jul 2019 09:01:02: start X-correlation... INFO @ Fri, 05 Jul 2019 09:01:02: end of X-cor INFO @ Fri, 05 Jul 2019 09:01:02: #2 finished! INFO @ Fri, 05 Jul 2019 09:01:02: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 09:01:02: #2 alternative fragment length(s) may be 1,133,295,501 bps INFO @ Fri, 05 Jul 2019 09:01:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.20_model.r INFO @ Fri, 05 Jul 2019 09:01:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:01:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:02:06: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:02:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:02:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:02:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:02:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.05_summits.bed INFO @ Fri, 05 Jul 2019 09:02:19: Done! pass1 - making usageList (58 chroms): 3 millis pass2 - checking and writing primary data (3338 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.10_summits.bed INFO @ Fri, 05 Jul 2019 09:02:45: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (636 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:02:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:02:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:02:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102001/ERX102001.20_summits.bed INFO @ Fri, 05 Jul 2019 09:02:55: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。